make.shared.gene.matrix: Count Shared Specimens Between Loci

In andrew-hipp/morton: Tools for manipulation of phylogenetic, genetic, and other biodiversity data

Count Shared Specimens Between Loci

Description

Using the output of make.gene.matrix, creates a gene matrix which summarizes the number of specimens shared between all pairs of gene loci.

Usage

make.shared.gene.matrix(dat, loci = dimnames(dat)[[2]][!dimnames(dat)[[2]] %in% c("orgs", "ncbiAcc", "numberOfOrgs", "numberOfAccessions", "numberOfSequences")])

Arguments

dat	The output of make.gene.matrix, a matrix linking gene sequence, specimen voucher, and gene locus.
loci	An optional vector of strings, the names of loci to include when counting shared specimens between pairs.

Details

loci includes all loci by default.

Value

A matrix of numeric values, where both rows and columns are loci and cells contain the number of individuals shared between two loci.

Author(s)

Andrew Hipp and Kasey Pham

See Also

make.gene.matrix

andrew-hipp/morton documentation built on April 7, 2024, 12:15 p.m.